Genetic diversity and phylogeography of Siberian roe deer,Caproulus pygargus,in central and peripheral populations

Current understanding of phylogeographical structure and genetic diversity of Siberian roe deer remains limited mainly due to small sample size and/or low geographical coverage in previous studies. Published data suggest at least two phylogroups: western (Ural Mountains and Western Siberia) and eastern (east from lake Baikal, including the Korean peninsula), but their phylogenetic relationship remains unclear. Combined sequences of cytochrome b (1140 bp) and the mtDNA control region (963 bp) were analyzed from 219 Siberian roe deer from 12 locations in Russia, Mongolia, and South Korea, which cover a large part of its range, to assess genetic diversity and phylogeographical status. Special emphasis was placed on the demographic history and genetic features of central, peripheral, and isolated populations. Results of median‐joining network and phylogenetic tree analyses indicate that Siberian roe deer from the Urals to the Pacific Ocean are genetically diverse and that geographical distribution and composition of haplogroups coincide with previously described ranges of the subspecies Capreolus pygargus pygargus and Capreolus pygargus tianschanicus. We found that peripheral populations in the northwestern parts of the species range (Urals), as well as the isolated population from Jeju Island, are genetically distinct from those in the core part of the range, both in terms of genetic diversity and quantitative composition of haplogroups. We also found that northwestern (Urals) and northern (Yakutia) peripheral populations share the same haplogroup and fall into the same phylogenetic clade with the isolated population from Jeju Island. This finding sheds light on the taxonomic status of the Jeju Island population and leads to hypotheses about the discordance of morphological and genetic evolution in isolated populations and specific genetic features of peripheral populations.     

Comparison of genetic diversity in the two arctic–alpine plants Diapensia lapponica var. obovata (Diapensiaceae) and Empetrum nigrum var. japonicum (Empetraceae) between Sakhalin in Russian Far East and Jeju Island in Korea, the southernmost edge of their distribution range

We compared allozyme variation in the two arctic–alpine plants Diapensia lapponica var. obovata and Empetrum nigrum var. japonicum between Sakhalin Island in Russian Far East, within their range core, and the Korean island of Jeju, their world’s southernmost distribution. For D. lapponica var. obovata, Sakhalin populations harbored moderate levels of within-population genetic variation and low among-population divergence, whereas extremely low levels of within-population genetic diversity and high among-population differentiation were found in Jeju Island populations. In contrast, we found moderate levels of within-population variation and low among-population differentiation in E. nigrum var. japonicum in both northern populations (those of Sakhalin and an additional population from northern Japan) and Jeju Island populations. Under a similar scenario of immigration history of arctic–alpine plants on Jeju Island during the glacial periods of the Pleistocene and local persistence through glacial/interglacial cycles, the contrasting genetic structure between D. lapponica var. obovata and E. nigrum var. japonicum is mainly attributable to their different life-history, ecological, and demographic traits: (1) hermaphroditic versus monoecious, dioecious or polygamous, (2) seeds with no adaptations for long-distance dispersal versus berry-like drupes dispersed by animals and birds, and (3) a very small patch near the peak of Mt. Halla with a few hundred individuals versus a relatively continuous distribution around the peak of Mt. Halla with numerous individuals. From a conservation perspective, in situ and ex situ conservation measures should be strengthened for D. lapponica var. obovata on Jeju Island given their extreme rarity there.     

Genetic diversity and historical migration patterns of an endemic evergreen oak,Quercus acuta,across Korea and Japan,inferred from nuclear microsatellites

Forests dominated by broad-leaved evergreen trees cover a narrow zone of the southern coast of Korea as well as warm-temperate and subtropical regions of Japan. However, little is known about their establishment history, especially in Korea. Endemic Quercus acuta grows in Korea and Japan. We evaluated its genetic diversity, population structure, and degree of lineage admixture in terms of its distribution history. Analyses utilized seven nuclear microsatellites that were genotyped from 330 individuals of 16 populations. Genetic diversity was highest for the Japanese Kyushu populations. The allelic diversity of populations was similar between Jeju Island and Kyushu, implying that they are putative refugia. Although the mean F _ST value was very low, patterns for isolation-by-distance were strong and significant. Results from Bayesian clustering and Monmonier’s algorithm indicated that populations are roughly partitioned from west (Korea and Kyushu) to east (Japanese Honshu). Therefore, the two divisions within this species are demographically independent and may have arisen due to past fragmentation. In considering the mixed genetic structure between Korea and Kyushu populations, and the higher levels of genetic diversity in mainland Korea relative to Honshu, we hypothesized that this species has been able to survive within Jeju Island and Kyushu. Consequently, mainland Korea populations might have been shaped by range expansion that kept them well mixed from a continuous and large genetic resource.     

Study of the independent gametophytes found on Jeju Island in South Korea and the first record of the obligate independent gametophyte of Antrophyum obovatum Baker

Fern gametophytes have often been neglected in research; however, studies on gametophytes are crucial for a better understanding of the evolution of ferns. During their life cycle, some gametophytes produce large and long‐lived populations without producing sporophytes and reproduce independently through asexual means, such as through the formation of gemmae. In this study, we investigated independent gametophytes on the Jeju Island of Korea, which was located on the land bridge between East China and Japan during the glacial periods. Fourteen gametophyte populations were collected from seven sites, of which 13 populations were clearly identified as belonging to four fern species known to occur in Jeju Island with BLAST searches using rbcL and trnL‐F sequences. Surprisingly, the last remaining population constituted undescribed taxa in Korea. We presented the first report of the independent gametophytes of Antrophyum obovatum Baker which has not been previously recorded in Korea. It has been supposed that many ferns sought suitable habitat throughout the land bridge between China and Japan. However, Jeju Island might be unsuitable for vittarioid ferns that prefer a tropical or subtropical environment. Consequently, only two species of vittariod ferns (A. obovatum and Haplopteris flexuosa (Fée) E.H. Crane) in the form of a gametophyte and sporophyte, respectively, exist on Jeju Island. Therefore, this gametophyte population must be protected and managed from a conservation perspective. In the case of the independent gametophyte of Hymenophyllum wrightii Bosch, haplotype analysis was conducted based on the rbcL sequences and the result supported that the North American populations were migrated from Japan through land bridge during the glacial periods and Jeju populations were recently established by long‐distance dispersal of the Japanese populations.     

The distribution of diploids and polyploids of the Scilla scilloides complex in Korea

A total of 3 384 individuals of Scilla scilloides Druce were sampled from 40 natural populations at 35 different localities over the Korean Peninsula and analysed cytogenetically. The following cytogenetic types were found: AA (19.6%), AABB (72.4%), ABBB (4.3%), AABBB (3.0%) and aneuploids (0.8%). Of these, AA was found in 9 populations along the west side of the Korean Peninsula facing the Yellow Sea and on Yeongdo and Jeju Islands. Type AABB, the most common type in the complex, was found in 33 natural populations on the Korean Peninsula and Jeju Island. The distributions of ABBB and AABBB are restricted to the southern part of the Korean Peninsula and Jeju Island; they were found in 8 natural populations. In southern Korea the above four types showed overlapping distribution and two or three were often found growing together.Genome A, occurring in the three allopolyploids in the Korean Peninsula, was the same as that in allopolyploids in Japan. However, genome A occurring as AA diploids was karyotypically different from that in the allopolyploids. On the basis of distribution patterns and cytological features, the origin of the allopolyploids is discussed.     

Genetic variation and Wolbachia infection status of the lycaenid butterfly Zizina emelina (Lepidoptera,Lycaenidae) from Korean populations

The lycaenid butterfly Zizina emelina emelina (de l’Orza) (previously Zizina otis emelina; Lepidoptera, Lycaenidae) has populations distributed across Japan and Korea. Zizina emelina is listed on Japan’s Red List as an endangered species, owing to the loss of its principal plant food and habitat. Researchers previously investigated the genetic diversity and structure in Japanese populations by using mitochondrial and nuclear DNA analyses alongside their Wolbachia infection status to consider the conservation strategy. In this study, we investigated the genetic variation and Wolbachia infection status of Korean populations and compared our findings with these traits in the Japanese populations. Four novel mitochondrial haplotypes were found in the Korean populations, whereas nuclear DNA analysis revealed one new haplotype and another that matched the one reported previously in Japan. The two known strains of Wolbachia in the Japanese populations were also found in the Korean ones. Mitochondrial DNA analysis demonstrated that no gene flow had occurred between the Japanese and Korean populations. The fact that they share the same nuclear haplotype and Wolbachia strains, however, indicates a low level of population differentiation between the two.     

Molecular Systematic Study of <Emphasis Type="Italic">Chrysosplenium</Emphasis> Series <Emphasis Type="Italic">Pilosa</Emphasis> (Saxifragaceae) in Korea

To address systematic issues pertaining to series Pilosa of Korean Chrysosplenium, the phylogenetic relationships of the 35 accessions of Korean Chrysosplenium taxa were examined using the DNA sequence data obtained from the nuclear ribosomal internal transcribed spacer (ITS) regions and the psbK-I gene of the plastid genome. The results from both ITS and psbK-I sequence data indicated that Chrysosplenium flaviflorum formed a well-supported clade that merits species status of the taxon. The ITS phylogenetic trees detected two distinct lineages in Chrysosplenium pilosum var. fulvum. Geographically, one lineage was widely distributed throughout the country whereas the other was confined to Gyeonggi and Gangwon provinces. The plants sampled from Jeju Island, which have been recognized as C. pilosum var. sphaerospermum [C. hallaisanense] exhibited no DNA sequence feature segregating them from C. pilosum var. fulvum [C. barbatum] distributed in the mainland area of Korea. The plastid DNA sequence data was not fully in concordance with the nuclear ribosomal ITS data and the current taxa delimitation. These results suggest incomplete lineage sorting or that plastid genome capture may have occurred during the evolution of some taxa examined in the present study.     

Inter-specific relationships and hierarchical spatial genetic structuring in Nervilia nipponica, an endangered orchid in Japan

An understanding of the extent to which reproductive strategy and seed dispersal lead to the structuring of genetic diversity in space is required when planning measures towards the conservation of endangered plant species. In this study, genetic structure in the endangered terrestrial orchid Nervilia nipponica was investigated using amplified fragment length polymorphisms following extensive sampling throughout the species’ range in Japan and intensive sampling at a single population. Limited diversity was found within the species as a whole, but significant structuring was detected between populations. One genotype was common to two widely separated sites, possibly indicative of long-range dispersal. Significant structure was also detected at the intensively sampled site, as a result of the presence of two distinct putative clones. These findings are consistent with observations of the species’ ability to set seed autogamously and propagate vegetatively. Given the strong colonising capability inferred for the species, attention should focus on identifying and securing habitat conditions conducive to seed germination and seedling establishment in the development of a conservation strategy. As presently circumscribed, N. nipponica is shown to comprise two polyphyletic taxa, both endemic to Japan, and both distinct from N. taiwaniana, a species that some authors have considered conspecific.     

Two New Halogenated Compounds from the Marine Red Alga Laurencia nipponica Yamada from the Kunashiri and Etorofu Islands

The red alga Laurencia nipponica comprises various chemical races distributed relative to the ocean current in Japanese coastal areas. We investigated the chemical compositions and chemical races of L. nipponica distributed from the Kunashiri and Etorofu Islands, the confluence of the Soya warm current and Oya-shio cold current. Two new halogenated secondary metabolites, deacetylneonipponallene ( 1 ) and neopacifenol ( 2 ), along with four known compounds, deoxyprepacifenol ( 3 ), pacifenol ( 4 ), halo-chamigrene diether ( 5 ), and isolaurallene ( 6 ) were isolated from L. nipponica collected at Chikappunai, Kunashiri Island, while Zaimokuiwa (Kunashiri Island) and Sana (Etorofu Island) populations contained 3 , 7-hydroxylaurene ( 7 ), 2,10-dibromo-3-chloro-9-hydroxy-α-chamigrene ( 8 ), and (3Z)-laurefucin ( 9 ). The structures of 1 and 2 were established using spectroscopic methods. The chemical races of L. nipponica distributed in this area were divided into 6 - and 9 -producing races. Interestingly, both races contained 4 as an additional race-index, as well as its derivatives, 2 and 5 . To the best of our knowledge, this is the first example of a race comprising a mixture of two race-index compounds, suggesting that the convergence of two currents causes the production of new and diverse chemical races in this species.     

The Effects of Climate Change and Globalization on Mosquito Vectors: Evidence from Jeju Island,South Korea on the Potential for Asian Tiger Mosquito (Aedes albopictus) Influxes and Survival from Vietnam Rather Than Japan

Background

Climate change affects the survival and transmission of arthropod vectors as well as the development rates of vector-borne pathogens. Increased international travel is also an important factor in the spread of vector-borne diseases (VBDs) such as dengue, West Nile, yellow fever, chikungunya, and malaria. Dengue is the most important vector-borne viral disease. An estimated 2.5 billion people are at risk of infection in the world and there are approximately 50 million dengue infections and an estimated 500,000 individuals are hospitalized with dengue haemorrhagic fever annually. The Asian tiger mosquito (Aedes albopictus) is one of the vectors of dengue virus, and populations already exist on Jeju Island, South Korea. Currently, colder winter temperatures kill off Asian tiger mosquito populations and there is no evidence of the mosquitos being vectors for the dengue virus in this location. However, dengue virus-bearing mosquito vectors can inflow to Jeju Island from endemic area such as Vietnam by increased international travel, and this mosquito vector''s survival during colder winter months will likely occur due to the effects of climate change.

Methods and Results

In this section, we show the geographical distribution of medically important mosquito vectors such as Ae. albopictus, a vector of both dengue and chikungunya viruses; Culex pipiens, a vector of West Nile virus; and Anopheles sinensis, a vector of Plasmodium vivax, within Jeju Island, South Korea. We found a significant association between the mean temperature, amount of precipitation, and density of mosquitoes. The phylogenetic analyses show that an Ae. albopictus, collected in southern area of Jeju Island, was identical to specimens found in Ho Chi Minh, Vietnam, and not Nagasaki, Japan.

Conclusion

Our results suggest that mosquito vectors or virus-bearing vectors can transmit from epidemic regions of Southeast Asia to Jeju Island and can survive during colder winter months. Therefore, Jeju Island is no longer safe from vector borne diseases (VBDs) due to the effects of globalization and climate change, and we should immediately monitor regional climate change to identify newly emerging VBDs.     

New Record of the Family Lasiochilidae Carayon, 1972 (Hemiptera: Cimicoidea) from the Korean Peninsula,with Re-Description of Lasiochilus (Dilasia) japonicusfrom Jeju Island

Herein, Lasiochilus (Dilasia) japonicus Hiura 1967 is recognized for the first time on the Korean Peninsula. This insect is a member of the Family Lasiochilidae, which is new to the Korean Peninsula. Both female and male adults are re-described on the basis of specimens obtained from Jeju Island, Korea.     

Norfolk Island Robins are a distinct endangered species: ancient DNA unlocks surprising relationships and phenotypic discordance within the Australo-Pacific Robins

Uncertain taxonomy hinders the effective prioritization of taxa for conservation. This problem is acute for understudied island populations in the southwest Pacific Ocean, which are increasingly threatened by habitat loss, predation and climate change. Here, we offer the first test of taxonomic limits and phylogenetic affinities of the iconic Pacific Robin radiation (Petroica multicolor) in order to prioritize the conservation of its nominotypical subspecies, the endangered Norfolk Island Robin (P. m. multicolor). We integrate phylogenetic analyses of ancient DNA and quantitative measures of plumage and morphometric variation to show that the Norfolk Island Robin should be recognized as a distinct species. Phenotypic and genetic datasets contradict the longstanding treatment of Pacific Robins (including Norfolk Island Robins) and Scarlet Robins (P. boodang) as a single species. Instead, we show that Norfolk Island Robins are deeply divergent from Scarlet Robins and have more genetic similarity to Red-capped Robins (P. goodenovii) than to other Pacific Robins. This finding is unrepresentative of the current taxonomic and conservation status of the Norfolk Island Robin, which we propose should be recognised as an endemic endangered species. Our study clearly shows that in the absence of contemporary tissues, ancient DNA approaches using historical museum specimens can address taxonomic questions that morphological traits are unable to resolve. Further, it highlights the need for similar studies of other threatened Norfolk fauna with uncertain taxonomic status in order to ensure appropriate conservation prioritization.     

Phytogeochemical,geographical and vulnerability study of the Paleosubtropical element <Emphasis Type="Italic">Notholaena marantae</Emphasis> subsp. <Emphasis Type="Italic">marantae</Emphasis> (Sinopteridaceae) at the western edge of its range

Serpentine outcrops are distinct from their background geological context, as they are often isolated from one another, and provide a home to a significant number of rare or endemic taxa. The aim of this study was to assess the Portuguese populations of one such taxon, Notholaena marantae subsp. marantae, including information on its biogeography, habitat, geographical range and conservation status. A detailed study was also made of the endemic association Notholaenetum marantae, a member of the Phagnalo saxatilis-Cheilanthion maderensis alliance, a type of vegetation included in the EU Habitats Directive 92/43/ECC. The distribution of Notholaena marantae was highly fragmented, with two sites accounting for over 50% of the total number of individuals recorded. The presence of N. marantae is associated with that of ultramafic rocks, which show specific geochemical features. The conservation status of the species is a cause for concern. We propose that the species be considered ‘vulnerable’ according to the criteria of the IUCN (2001), and that areas where its populations grow be protected. This study confirms the endemic status of N. marantae subsp. marantae in Portugal and the importance of the conservation of its serpentine habitats.     

Phylogeography and genetic diversity of East Asian Neolitsea sericea (Lauraceae) based on variations in chloroplast DNA sequences

Neolitsea sericea is an evergreen broad leaved tree in the warm-temperate regions of East Asia. This area is a hotspot for plant species richness and endemism caused by dynamic changes in land configuration during the Quaternary. However, the historical migration of such evergreen tree species is still poorly understood. In an attempt to reconstruct the phylogeographic history of N. sericea during the Quaternary, we identified the chloroplast DNA haplotypes of 287 individuals from 33 populations covering almost all of its geographic range. Analyses were based on sequence data from the trnL–F, psbC–trnS, and rps16 regions. Nine haplotypes were identified. The majority included ancestral types in the southwestern part of the main islands of Japan, with other region-specific haplotypes being found in populations on the Korean Peninsula, Taiwan (Isl. Lanyu), and elsewhere in Japan. A statistical parsimony network revealed two lineages derived from Japanese main islands. One was represented on the Korean Peninsula, the other on Isl. Lanyu. The current distribution of N. sericea has been shaped by colonization via land bridges. During the glacial periods, two primary, but separate migration routes were followed—from the southwestern part of the Japanese main islands to either the Korean Peninsula or Taiwan. In addition, we believe the Zhoushan populations were shaped by post-glacial processes through an ECS land bridge (East China Sea basin) from northern refugia that existed during the late Pleistocene.     

Distributional range extension of the seagrass Halophila nipponica into coastal waters off the Korean peninsula

Eight temperate seagrass species (five in the genus Zostera, two in the genus Phyllospadix, and Ruppia maritima) have been previously reported in coastal waters off the Korean peninsula, which lies between 33°N and 43°N. Recently, a species of Halophila, a genus which occurs predominantly in tropical and subtropical areas, has been observed on the southern coast of Korea for the first time. The species was identified as Halophila nipponica. H. nipponica is distributed in warm temperate regions of Japan influenced by the warm Tsushima Current and was previously unknown outside the Japanese archipelago. Thus, we are able to report a range extension into Korea. The Korean Halophila meadow that we observed covered an area of about 2.1 ha, with average shoot density of about 1300 m⁻². We measured morphological features of vegetative and reproductive organs between June and September 2007. Morphological and reproductive features of the Halophila species in Korea were similar to those of the species in Japan. Increased water temperature in the coastal waters of Korea may at least partially account for the persistence of this new population.     

Genetic assessment of <Emphasis Type="Italic">Abies koreana</Emphasis> (Pinaceae), the endangered Korean fir,and conservation implications

To establish a management plan for endangered and rare species, genetic assessment must first be conducted. The genetic characteristics of plant species are affected by demographic history, reproductive strategy, and distributional range as well as anthropological effects. Abies koreana E. H. Wilson (Pinaceae), Korean fir, is endemic to Korea and found only in sub-alpine areas of the southern Korean Peninsula and Jejudo Island. This species has been designated as critically endangered by the International Union for Conservation of Nature due to a continuous decline in its range and population fragmentation. We genotyped 176 individuals from seven natural populations and two afforested populations on the Korean Peninsula using 19 microsatellite loci. STRUCTURE analysis revealed two genetic clusters in natural populations (F _st  = 0.040 and R _st  = 0.040) despite low differentiation. We did not detect a significant reduction in genetic diversity or the signature of a genetic bottleneck despite population fragmentation and small population size. We deduced that this species exhibits a metapopulation structure, with the population on Jirisan Mountain acting as a source of genetic diversity for other local small populations on the Korean Peninsula, through contemporary asymmetric gene flow. However, the majority of afforested individuals on the Korean Peninsula originated from a different gene cluster. Thus, we recommend a conservation strategy that maintains two genetically unique clusters.     

Phylogeography of the eight-barbel loach <Emphasis Type="Italic">Lefua nikkonis</Emphasis> (Cypriniformes: Nemacheilidae): how important were straits in northern Japan as biogeographical barriers?

Many straits in the Japanese archipelago have been proposed as biogeographical boundaries, but there is disagreement regarding their importance as historic barriers against dispersal of terrestrial and freshwater taxa. Mitochondrial DNA haplotype and phylogenetic analyses of Lefua nikkonis, a primary freshwater fish inhabiting northern Japan and descendent from Siberia, revealed that the species is genetically structured within its geographic range, but that two major haplotypes are widely distributed across the Ishikari Lowland of Hokkaido Island as well as across the Tsugaru Strait between Hokkaido and Honshu Islands, two well-known biogeographical boundaries of northern Japan. The two major haplotypes were separated from each other by only one mutational step, and many other haplotypes, including those endemic to the region south of these barriers, have diverged from the major haplotypes, suggesting rapid range expansion and local differentiation. Divergence-time estimates, based on vicariance of the Honshu endemic congener L. echigonia via uplift of the Central Highlands, demonstrated that the southward dispersal of L. nikkonis from Hokkaido Island to Honshu Island occurred less than 0.08–0.19 Mya, suggesting that a land bridge emerged at the Tsugaru Strait during the Riss glaciation. Given that other freshwater taxa crossed the strait earlier (during the Middle Pleistocene), it is likely that land bridges in the strait have repeatedly emerged. The fact that L. nikkonis invaded only the northern part of Honshu, and that many other freshwater species also have the limit of their distribution ranges in this area as well, indicates that a faunal transition zone might persist even without the Tsugaru Strait. Thus, straits and lowlands in northern Japan are likely to have been less important as dispersal barriers to freshwater taxa than is currently thought.     

Genome-wide detection and characterization of positive selection in Korean Native Black Pig from Jeju Island

Background

In the 1980s, Korean native black pigs from Jeju Island (Jeju black pigs) served as representative sample of Korean native black pigs, and efforts were made to help the species rebound from the brink of extinction, which occurred as a result of the introduction of Western pig breeds. Geographical separation of Jeju Island from the Korean peninsula has allowed Jeju black pigs not only to acquire unique characteristics but also to retain merits of rare Korean native black pigs.

Results

To further analyze the Jeju black pig genome, we performed whole-genome re-sequencing (average read depth of 14×) of 8 Jeju black pig and 6 Korean pigs (which live on the Korean peninsula) to compare and identify putative signatures of positive selection in Jeju black pig, the true and pure Korean native black pigs. The candidate genes potentially under positive selection in Jeju black pig support previous reports of high marbling score, rare occurrence of pale, soft, exudative (PSE) meat, but low growth rate and carcass weight compared to Western breeds.

Conclusions

Several candidate genes potentially under positive selection were involved in fatty acid transport and may have contributed to the unique characteristics of meat quality in JBP. Jeju black pigs can offer a unique opportunity to investigate the true genetic resource of once endangered Korean native black pigs. Further genome-wide analyses of Jeju black pigs on a larger population scale are required in order to define a conservation strategy and improvement of native pig resources.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-014-0160-1) contains supplementary material, which is available to authorized users.     

Detection of Ancestry Informative HLA Alleles Confirms the Admixed Origins of Japanese Population

The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago.